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Sgt. Malcolm "Mal" Reynolds, Zoë, and several fellow soldiers are part of an attempt to prevent Alliance forces from taking Serenity Valley. Mal sends a squadron up to high ground while he, Zoë, and another soldier, Bendis, attempt to capture an Alliance anti-aircraft gun in order to take out an airborne skiff that's preventing reinforcements from arriving. Despite Bendis suffering from shell-shock, Zoë is able to provide the cover fire Mal needs, and he succeeds in commandeering the weapon and shooting down the skiff. However, the air support that they need to get out of the valley does not arrive. Instead, the Alliance has taken the valley, and the rebels are ordered by their command to surrender.

Mal is captain of his own transport ship, the Firefly-class Serenity, and Zoë is his second-in-command. He, Zoë, and Jayne are attempting to melt open the hatch of an abandoned wreck of a carrier in space. Wash is on Serenity in the pilot's station keeping watch when he detects a Tohoku-class cruiser, the I.A.V. Dortmunder, approaching them and the wreck. He contacts Mal, who tells him to cut all power on Serenity to escape detection. Wash tells the ship's engineer, Kaylee, to shut everything down. The cruiser detects some residual heat from Serenity, and they actively begin scanning. Caught in the act, the Serenity crew double-times loading the cargo while the cruiser deploys gunships to stop them. Mal has Wash engage the "crybaby", a decoy distress beacon whose transmission is mistaken by the Dortmunder to be another ship in trouble. Mal gets his team and cargo on board and signals Wash, who turns Serenity away from the cruiser and speeds away. The cruiser halts deployment of the gunships so that it can go help the "other ship", but does put out a bulletin that a Firefly-class ship is carrying stolen Alliance goods.

Inspecting the cargo, Mal seems troubled by the fact that the cargo, which consists of hundreds of unidentified bars, are stamped by the Alliance. The crew starts hiding the cargo as Mal has Zoë contact Badger, their fence on Persephone, that the job is done. Zoë and Wash leave for the bridge. Mal announces that they will be taking on passengers on Persephone before heading to Boros. Mal asks if Inara has checked in, and when he is told she hasn't, he asks them to let her know that a speedy departure from Persephone might be needed.

Inara, apparently a prostitute (though the official title is "Companion"), finishes up her session with an unworldly young Alliance officer, who awkwardly offers to rescue her from her lifestyle. After he leaves, Inara contacts Serenity and is instructed to meet at the Eavesdown Docks.

Serenity lands on Persephone and the various crew members split up; Kaylee stays around to find passengers, Wash takes Serenity's utility vehicle to get supplies, and Mal, Zoë, and Jayne go to speak with Badger. Badger is not happy that Mal's team got caught in the salvage operation, even though they weren't identified, because the cargo is "molecularly stamped" and can be traced. He refuses to take the cargo or pay for it, much to the anger of Serenity's crew. Guns are drawn, but Badger's men outnumber the Serenity crew and, after Badger smugly insults Mal, the crew are forced to leave empty-handed.

A pious religious man named Shepherd Book encounters Kaylee, who notices that he's looking at the ships and not their destinations. He tells her that he's a "shepherd" from the Southdown Abbey, has been there for a while, and has decided it's time for him to be "in the world". He's got a little bit of money, but he also has something in a small box which he shows her, which seems to impress her.

Mal and company discuss how to unload their cargo while returning to Serenity. Despite being shot by her in the past, Mal decides to try selling it to a woman named Patience on a terraformed moon called Whitefall, despite Zoë's objections. As the crew all arrive at Serenity new passengers are coming on board, including a man named Dobson, and a wealthy doctor named Simon. Zoë is not happy about having a bunch of passengers sitting on top of their stolen cargo, but Mal quietly laughs it off. Inara arrives in her shuttle, and the crew and passengers prepare to take off.

In flight, Mal, Kaylee, and Zoë lay out the ground rules. Mal, who appears to be antireligious, learns that Book is a shepherd, but Kaylee assures everyone that it's not a problem. Wash arrives and Mal covers up the illicit nature of their impending transaction by telling the passengers that the ship's been ordered by the Alliance to take some medical supplies to Whitefall, the fourth moon of Athens, so they'll be going there before heading off to Boros.

In the cargo bay, Inara exits her shuttle and Mal introduces her to Book, referring to her somewhat half-seriously as an "ambassador". Book takes this literally, which Mal finds amusing. When Mal explains that she is a "whore", Kaylee corrects him that the term is "Companion". Mal goes on to explain that in some ways a Companion is an ambassador, since her respectable and high-class presence causes doors to open that would otherwise be closed; Companions, it seems, have more in common with geisha or courtesans than street hookers. Mal baits Book a little more before Inara politely returns to her shuttle (although she does have a few stinging words for Mal).

Kaylee starts making dinner and we see that Book's box contains ripe strawberries, one of which Kaylee eats lovingly. Later, the passengers and most of the crew settle down to dinner, including fresh vegetables donated by Shepherd Book, Zoë taking a plate to Wash on the bridge. Book asks if anyone minds if he says grace, and Mal replies 'Only if you say it out loud'. After a silent grace joined by most of the crew, Simon asks if the Alliance often commandeers Serenity, and the passengers and crew talk about the political climate and physical difficulties of the border worlds. Kaylee seems to be taken by Simon, which amuses Jayne, who makes several rude comments in that regard. Mal reacts by ordering him out of the dining area, though not without protest from Jayne.

Inara is in her shuttle giving herself a sponge bath when Book arrives with some supper. He's a little embarrassed and Inara covers up, expecting a sermon on her wickedness. He puts her at ease with slightly self-deprecating humor, and they move on to discussing the mystery that is Malcolm Reynolds. Meanwhile, Wash summons Mal to the bridge. Arriving on the bridge, Wash tells Mal that someone on board sent a message to a Tohoku-class cruiser. He scrambled it as best he could, but still, there's a mole on the ship.

Thinking Simon is the mole, Mal finds him in the cargo bay inspecting a large high-tech crate and punches him, then confronts him at gunpoint, accusing him of being a "Fed", or member of the Alliance. Book appears, and points out to Mal that Dobson is on a catwalk, pointing a gun at Mal and Simon. Dobson informs Simon that he is bound by law, the customary statement made when Alliance authorities arrest someone. Apparently Simon is wanted by the Alliance for something. Moreover, he plans on prosecuting the crew for transporting a fugitive across interplanetary borders and isn't convinced that they are actually transporting medical supplies. Mal urges Simon to stand down while Book tries to calm everyone down. Kaylee and Jayne suddenly enter, and the jumpy Dobson reacts by shooting Kaylee in the stomach. Mal and Book overpower Dobson, and Simon goes to Kaylee's side to look at her wound. Jayne makes to shoot Dobson, but Book refuses to let him do so. Zoë appears and orders Jayne to tie up Dobson. Mal intends to hand Simon over to a Tohoku-class cruiser, but Simon threatens to not treat Kaylee if he does so and tells Mal to flee. After a tense moment, Mal reluctantly agrees.Simon works on Kaylee in the infirmary, removing the bullet fragments, but tells Mal that only time will tell if she will heal fully.

After coming out of cryogenic sleep River is horribly confused and frightened. Simon quickly goes to her and heavily reassures River that everything is fine and that she is safe.

Curious as to why the Alliance wanted Simon, Mal goes to the cargo bay, opens Simon's crate while Jayne restrains Simon, and finds a young nude girl inside. Mal assumes that she is a slave, but after the girl gains consciousness and starts screaming, Simon goes to her to calm her down, explaining to the others that the girl is River Tam, his sister. Later, he further explains that she was born with a gifted intellect in diverse fields such as physics and dance, dwarfing his own talents, and that she was sent to an Alliance-funded academy where she was subjected to some unspecified experiments. Simon rescued her from the Alliance's clutches and is on the run trying to protect her from them. Mal tells Simon he's leaving him and his sister at Whitefall, but that if Kaylee won't survive, he's "getting off a mite sooner." Inara tells Mal that if he expels Simon and River from the ship, that she'll leave too. Mal decides to proceed with the stolen goods sale to Patience on Whitefall.

Jayne interrogates Dobson to find out how much he was able to tell the Alliance about them and their destination before his transmission was cut. Dobson offers a bribe to Jayne, telling him that the Alliance will give him enough money for him to buy his own ship if he releases him. He also told Jayne his first name is "Lawrence."

Wash and Mal observe an old Trans-U approaching, and they realize it is a Reaver raiding party. Zoë explains to Simon that if the Reavers (whom Simon has only heard about in apocryphal stories) board the ship, everyone on Serenity will be raped to death, cannibalized, and have their skin sewn into the insides of the Reavers' clothing, and if they're 'very lucky, they'll do it in that order'. Luckily, the Reaver ship passes by.

In her shuttle, Inara gives Simon some of her immunization packs. Simon apologizes for his part in the current situation. Inara explains that he fits in with the rest of the crew. Mal arrives, and when Inara tells him that he's on her shuttle, Mal points out that she is merely renting the shuttle from him. She replies that he can enter it at will when she falls behind on rent.

On the bridge, Mal and Patience exchange some pleasantries over the comm as their exchange looms, but Mal thinks she's planning to shoot him again. Meanwhile, Dobson is cutting through his bindings.

Serenity lands on Whitefall. Mal and Zoë walk out into a valley to meet Patience and her henchmen, but not before Mal sends Jayne to take out any potential snipers. Mal gives Patience a sample of the cargo, which turns out to be nutritional/immunization bars, each one of which can feed an entire family for a month, or longer "if they don't like their kids too much." Patience attempts to renege on the deal, but Jayne, Mal and Zoë dispatch Patience and her gang, taking the money they were promised. Although, one of Patience's men shot Mal's arm, ripping a hole on his sleeve coat. Jayne then arrives, having been contacted by Wash with bad news: the Reavers followed them to Whitefall.

When Book goes to see Dobson, Dobson attacks Book, knocking him out, then hitting him a few more times out of anger. He goes to the infirmary and grabs River, but is discovered by Simon, who jumps from the catwalk over the cargo bay. After a brief struggle, Dobson gets hold of a gun and points it at River, but Mal arrives and, without breaking stride, shoots Dobson. They dump him off the ship as they prepare to leave, the Reavers on their tail. Mal orders the passengers to Inara's shuttle as Jayne carries the still-convalescing Kaylee to the engine room. With Book carrying out Kaylee's instructions and Wash's superb flying, Serenity pulls a "Crazy Ivan" maneuver, enveloping the Reaver ship in a fireball ignited by their exhaust, allowing them to escape.

Book goes to Inara and, in essence, tearfully confesses that he's terribly lost and might be on the wrong ship. Inara thinks he just might be exactly where he ought to be.

Simon and River finally reunite on Serenity

Back in the passenger quarters Simon tucks River in and says that they will find "A safe place." to live soon. River gently caresses her brother's face and says uncertaintly "I didn't think you'd come for me." (alluding to her being in the Academy.) Simon quips back affectionately "Well you're a dummy." The two then share a much relived hug properly reuniting at last after nearly three years apart.

On the bridge, Jayne tells Mal that River's in danger and that Dobson had told him the Alliance will keep after her. Mal asks if Dobson tried to bribe him, to which Jayne let him know it wasn't enough of a bribe, and that it'll be an interesting day if the bribe is ever big enough. Jayne leaves as Simon enters. Mal suggests to Simon that he and River might be safer on the move than hiding in one place, and points out that Serenity is always moving, and in need of a medic. Simon accepts his offer.

Won the Visual Effects Society's Best Visual Effects in a Television Series award, and was nominated for Best Compositing in a Televised Program, Music Video, or Commercial. Came second in the 2003 Hugo Best Dramatic Presentation, Short Form category; and was nominated for a Golden Reel Award by the Motion Picture Sound Editors, USA in the Best Sound Editing in Television Long Form: Sound Effects/Foley category.

According to Tim Minear, Inara's vial was to be revealed in a later episode to be able to kill whoever she has sex with. In the story, Inara uses the vial during a reaver attack, and when the crew finds her, all of the reavers are dead.[1]

Simon states in this episode that he had merely arranged for and funded River's escape from the Alliance, however this is seemingly retconned in the film of Serenity, when it is shown he was the one who broke her out of the facility.

When Inara's shuttle if you look closely at the top left hand side of Serenity, you can see a Star Wars imperial shuttle taking off, the same one from Return of the Jedi.

When Mal takes control of the AA turret, a Weyland-Yutani logo can be seen at the top of the turrets screen.

The scene where Inara boards Serenity and is introduced to the passengers was initially filmed with Inara's original actress Rebecca Gayheart in the role, however Joss Whedon already felt that Gayheart wasn't right in the role (due to a lack of energy with the other actors). Having already decided to replace her, Whedon then shot the scene entirely as single-shots only focusing on a single character, therefore when Morena Baccarin was cast it was simply a case of filming her lines rather than reshooting the entire sequence.

When applying "the sticky" to the ship's access panel, Mal traces a straight line towards the edge of the plate. Later shots of the plate show the compound curving sooner clockwise around the central point.

Wash is seen mimicking holding the flight controls near the end of the episode without actually holding them. The DVD commentary revealed the controls were too far away for the shot, but Joss really wanted the shot, so they moved Alan's chair back and had him mime the controls.

When piloting her shuttle on Persephone, Inara is holding the flight controls upside down. Joss Whedon calls attention to this in the DVD commentary.